ArticleThe journal of physical chemistry. B2016
Quantifying the Influence of the Crowded Cytoplasm on Small Molecule Diffusion.
Article in The journal of physical chemistry. B, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 46 citations in OpenAlex.
- Cytoplasmic crowding acts as a porous medium reducing macromolecule diffusion.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Bacterial cell volume regulation and the importance of cyclic di-AMP.Microbiology and molecular biology reviews : MMBR · 2024Review
- Physiology of intracellular calcium buffering.Physiological reviews · 2023Review
- Self-Organization of Enzyme-Catalyzed Reactions Studied by the Maximum Entropy Production Principle.International journal of molecular sciences · 2023Article
- Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling.Quarterly reviews of biophysics · 2023Review
- Postmortem changes in brain cell structure: a review.Free neuropathology · 2023Article
- Crowding within synaptic junctions influences the degradation of nucleotides by CD39 and CD73 ectonucleotidases.Biophysical journal · 2022Article
- Assessment of transient changes in oxygen diffusion of single red blood cells using a microfluidic analytical platform.Communications biology · 2021Article
- Moonlighting Proteins Shine New Light on Molecular Signaling Niches.International journal of molecular sciences · 2021Review
- Chromatin as a key consumer in the metabolite economy.Nature chemical biology · 2020Review
- Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide distributions.PLoS computational biology · 2020Article
- Cascade Kinetics in an Enzyme-Loaded Aqueous Two-Phase System.Langmuir : the ACS journal of surfaces and colloids · 2020Article
- Metabolic Compartmentalization at the Leading Edge of Metastatic Cancer Cells.Frontiers in oncology · 2020Review
- Increasing Salt Rejection of Polybenzimidazole Nanofiltration Membranes via the Addition of Immobilized and Aligned Aquaporins.Processes (Basel, Switzerland) · 2019Article
- Reaction and diffusion thermodynamics explain optimal temperatures of biochemical reactions.Scientific reports · 2018Article
- Metabolic regulation of transcription through compartmentalized NADScience (New York, N.Y.) · 2018Article
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
- Electrodiffusion phenomena in neuroscience: a neglected companion.Nature reviews. Neuroscience · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Cytosolic crowding can influence the thermodynamics and kinetics of in vivo chemical reactions. Most significantly, proteins and nucleic acid crowders reduce the accessible volume fraction, ϕ, available to a diffusing substrate, thereby reducing its effective diffusion rate, Deff, relative to its rate in bulk solution. However, Deff can be further hindered or even enhanced, when long-range crowder/diffuser interactions are significant. To probe these effects, we numerically estimated Deff values for small, charged molecules in representative, cytosolic protein lattices up to 0.1 × 0.1 × 0.1 μm(3) in volume via the homogenized Smoluchowski electro-diffusion equation. We further validated our predictions against Deff estimates from ϕ-dependent analytical relationships, such as the Maxwell-Garnett (MG) bound, as well as explicit solutions of the time-dependent electro-diffusion equation. We find that in typical, moderately crowded cell cytoplasm (ϕ ≈ 0.8), Deff is primarily determined by ϕ; in other words, diverse protein shapes and heterogeneous distributions only modestly impact Deff. However, electrostatic interactions between diffusers and crowders, particularly at low electrolyte ionic strengths, can substantially modulate Deff. These findings help delineate the extent that cytoplasmic crowders influence small molecule diffusion, which ultimately may shape the efficiency and timing of intracellular signaling pathways. More generally, the quantitative agreement between computationally expensive solutions of the time-dependent electro-diffusion equation and its comparatively cheaper homogenized form suggest that the latter is a broadly effective model for diffusion in wide-ranging, crowded biological media.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.